8b9a96d13e981345d9022639b4edd59c *DESCRIPTION
9628ad9ed64603f7ed017ba186bd6176 *NAMESPACE
e96382dfc876ba6af180a79ed52adbda *NEWS
a492484c01e95e6d4723ad31b10e671f *R/RcppExports.R
9a4350ba731a30b8eb18161a103530ce *R/crosses.R
c3e20272dfb6afa22f5b0730581ac2b3 *R/dataproc.R
66ba575bbcff51cb00569fe2dc54cf58 *R/datatools.R
013e0fd897ee362b272da37af121badc *R/diversity.R
6a04feee2516a91b64f1cec9958b2462 *R/docdata.R
a186e0ffef28efdc7076680391c58c2d *R/filters.R
18d7cf76bf4e751aefadf8a6f64e3347 *R/graph.R
94a54605f8dbf8536c5a601622e876c3 *R/infoanalysis.R
e4dc5693adee067e4cfa939fe431b449 *R/input.R
9f8d30d8e0cade55c27ab0dda451755a *R/kmers.R
ef81c66aa4f2c28c94dd9b4dd0b0bb7c *R/measures.R
f29f5cddfe3ab5afebd426d69233010f *R/mitcr.R
ce67446ecea64be9cb65982f94d5c69a *R/plots.R
4bb2940356c4b42dce7771978f8fc794 *R/repdiversity.R
9691172943fdfcd13dc413e1d9091efb *R/repoverlap.R
8d3e77c60a736b2906e01eea58fbd177 *R/segments.R
0bac2b82ac075c676934af5dc34de7a8 *R/shared.R
d7cd7678241525666852f7f92a2c03c2 *R/spectrum.R
991c25e078ad053b7860dcd3a91a1697 *R/stats.R
eff90f75acf7f2a06b720cce2abb0840 *R/strtools.R
c2caff95e6f02399c43ac4550ca928c8 *README.md
93e0c1cee03d5bb7add82b8101c81305 *build/vignette.rds
89d6d3f555bed92c5ed36af98b04c7a4 *data/beta.prob.rda
0b472b1afd448af9612974a7033a82bb *data/datalist
3e5199fd3d3acb248adfe09b59f39bfd *data/genesegments.rda
a210524a6d7f8f05e66f1ec59416ddc7 *data/twa.rda
8253da4f56f8eee73ad14945e15ab374 *data/twb.rda
249c46d9eba32c05a7623717ca773160 *inst/CITATION
8dd437aa67de610b66bd177f3aa5ea6b *inst/crossanalysis.report.Rmd
b3e30dfc5fa127c08986ec4efbf74f9b *inst/doc/tcrvignette.R
6efbf60e3b82c3c74bae216ac43057de *inst/doc/tcrvignette.Rmd
ad12500fe7b1e488ea40a9774f45253f *inst/doc/tcrvignette.html
0d8030aaef0685c2f34fc53cce1adfac *inst/library.report.Rmd
32483ea4e5953ef574de5146f416f260 *man/AA_TABLE.Rd
3ad08b613dfb52056f1f70af21351209 *man/apply.symm.Rd
666fbdc234324507413b9302055a7f53 *man/assymetry.Rd
13d41dab18f37567433cad27b29983f0 *man/barcodes.to.reads.Rd
81291046d8e27600d305d50172ca77ae *man/beta.prob.Rd
9ff8860a50d67ca861e16cb31554fd02 *man/bootstrap.tcr.Rd
f01a8f752c5efdc8dda853bf71830263 *man/check.distribution.Rd
1ec8c410a7c393927ff410066a5f5e30 *man/clonal.space.homeostasis.Rd
08b8a6de237fc189aa67f5d4644561ea *man/cloneset.stats.Rd
8b2b0d8773f2e557aef60f75aad41f43 *man/codon.variants.Rd
226417d0c8a0fb9b7065ddc9772e5e51 *man/column.summary.Rd
b598bb429532ac94053c2dba4a76ce0c *man/contamination.stats.Rd
69a0b5e13ecd1ab73257db71edce312c *man/convergence.index.Rd
be5c3528d7afebc88d4fc70e7f85bb7d *man/cosine.sharing.Rd
45c83042422aee0228fe7393a285e853 *man/cosine.similarity.Rd
f5ad300945cff8b087ea3fa7a0c26ab0 *man/entropy.Rd
463837ada823ba992103a8ee5a9ea2c1 *man/entropy.seg.Rd
d618523d54b64d919d809b3420bbc29e *man/find.clonotypes.Rd
98c494ef88114e3b37dd3778ce31d900 *man/find.similar.sequences.Rd
a6f68f7ec92be4dcb112b9adb56238c3 *man/fix.alleles.Rd
aff69141f7f88070fb5387e16e945c37 *man/gc.content.Rd
3d2c9e3b2aa3a1dd1ad0f1a433711a57 *man/geneUsage.Rd
d49f480abf40ea96fde33252389fff4e *man/generate.kmers.Rd
717dfc91866d01c6da3640b4245e85b8 *man/generate.tcr.Rd
0849a7d3a7f089d76c0a704df08c4491 *man/get.all.substrings.Rd
01072fc63825d42c41f859c8456903b7 *man/get.deletions.alpha.Rd
10f9603324f02989bee8d0c23bce04c5 *man/get.inframes.Rd
86510b1aaefefe5d57f5b8c5de54e79e *man/get.kmers.Rd
f89209552b86f4cd718c63a80b5d0a7c *man/get.n.barcodes.Rd
c875aaceb6b9a94bd64ee2bfd07f02a6 *man/gibbs.sampler.Rd
0fdc9874e928541b8d7a820309393cb2 *man/group.clonotypes.Rd
f77a7a82bdf601f8a534c274fdca41b4 *man/has.class.Rd
24b7ed602ad42e476227de2fc731a715 *man/intersectClonesets.Rd
4c5f5d5c69f34fe4f73140148cd21c51 *man/inverse.simpson.Rd
b41ce765dd447ab770aecce28a8a7001 *man/kmer.profile.Rd
d47a24bc5aa033d54d34235dab720f51 *man/kmer.table.Rd
1bc410522aa1a218b012868892b1bd8f *man/loglikelihood.Rd
421913eded0d6b5036d26ffa872a0986 *man/matrixdiagcopy.Rd
c0ba43a7e5a5f1e133d9b42d6543caf1 *man/mutated.neighbours.Rd
4480cfc303b6e0158d38a9c7445b2848 *man/mutation.network.Rd
cadf2e9eb0a8111c347286c553c622d9 *man/parse.cloneset.Rd
5c9b80c1d77d08b9c0c40f21fb259368 *man/parse.folder.Rd
c5bbca410b20f02f2d5882af808d1893 *man/pca.segments.Rd
a7cc2994e8aef63eaeafdf304ada0518 *man/permutedf.Rd
213b3b053dfec3493a505da4b72cf6df *man/rarefaction.Rd
0836cbeac56d33f86b6ed67c38c6a12b *man/repDiversity.Rd
2291ab3761a2dd2a1fe874856656a877 *man/repOverlap.Rd
9bfcb7eb9d14691db4c886a7e9707377 *man/revcomp.Rd
fd7f8e0e2d45b9d6f68ca84c09021188 *man/reverse.string.Rd
53e35bf185eba18761df379f4bacbc98 *man/sample.clones.Rd
54a2c345d86947da1a8c62b77beca08d *man/sample2D.Rd
cde85ef9ed09ffd2f4abfca7f3143fdb *man/segments.alphabets.Rd
99e45fcbd285c3acee39c5180b4fca70 *man/segments.list.Rd
7c94619711c1c2e19802a178de2d0e13 *man/set.group.vector.Rd
5e5e00552c7c53086848eeac33f0e3c6 *man/set.pb.Rd
89518e394e8ab64c5473257867691d1c *man/set.people.vector.Rd
f766c29fe6175c5dfc00066ccb348f26 *man/set.rank.Rd
a4655812c5b96d5ade6efd5fc74d6357 *man/shared.repertoire.Rd
148f5013dd8b22f707d150586782ff62 *man/spectratyping.Rd
efb1be2589ab1b8fa6cb0205e0dbad64 *man/startmitcr.Rd
682d0d9089939e171193135942ea1ff2 *man/tailbound.proportion.Rd
f81b1c0475d32cd9f1dfc6c4db535633 *man/top.cross.Rd
057920e59c480b510b61cc21db9c9f44 *man/top.fun.Rd
3dd960c7cd5397d5e2aaa9da04ff3f09 *man/twinsdata.Rd
44605886ecbd0375635defef5e7eeb33 *man/vis.clonal.dynamics.Rd
fd09b686e371a87bfef6180ba9e9ec43 *man/vis.clonal.space.Rd
293ddf1b6c8b3f416a95210f93eadc4a *man/vis.count.len.Rd
084ae725927ee07d542f09eda252c045 *man/vis.gene.usage.Rd
c014b65818bb1e2c1fbfba7e831f647e *man/vis.group.boxplot.Rd
a6d7e1bab4e99561b05ef540b117bde2 *man/vis.heatmap.Rd
2b2f408144744480cf566e6912423487 *man/vis.kmer.histogram.Rd
00f8b215ba4348fae1840273a34d88c5 *man/vis.logo.Rd
1143ccf29bdc818be282fd20125c0a70 *man/vis.number.count.Rd
03d5d67f4111b5905e9e89bd32212e0b *man/vis.pca.Rd
cd9e1b27b2d3bddee072ddf056b8e800 *man/vis.radarlike.Rd
e7e4935b69f12ab55bd24b8b767a5822 *man/vis.rarefaction.Rd
a6002028b495f0b78c948cee79a89e7a *man/vis.top.proportions.Rd
e3d3cb360fbfdb3c6974e14eb5f09870 *src/Makevars
e69034809117f2a8b410ff83c0ffc74a *src/RcppExports.cpp
8613b0d97d73171a1f6a526d93a87ee9 *src/neighbour.search.cpp
6efbf60e3b82c3c74bae216ac43057de *vignettes/tcrvignette.Rmd
